Application of transcriptomics to compare the carbohydrate active enzymes that are expressed by diverse genera of anaerobic fungi to degrade plant cell wall carbohydrates

Anaerobic fungi within the phylum Neocallimastigomycota are found in the gut of heriborves. The efficiency with which the anaerobic fungi degrade plant biomass is well-recognized and recently has been the subject of renewed interest. To further understand the biological mechanisms anaerobic fungi isolated from the rumen use to break down lignocellulose, we employ a transcriptomic approach to examine carbohydrate digestion by Neocallimastix frontalis, Piromyces rhizinflata, Orpinomyces joyonii, and Anaeromyces mucronatus cultured on several carbon sources. Most of the predicted functions of the genes expressed are consistent across all four species which suggests they have evolved a similar strategy for successful colonization of the rumen and competition with other microbes for limited resources. The profile of enzymes involved in carbohydrate differed between species suggests that these organisms may be also display niche specialization which helps to reduce direct competition between different species of anaerobic fungi. All fungal species were found to express an extensive array of transcripts encoding carbohydrate active enzymes (CAZymes) ranging from 8.3 to 11.3% of the transcriptome. CAZyme families involved in hemicellulose digestion were the most abundant across all four fungi. This study provides additional insight into how anaerobic fungi have evolved to become specialists at breaking down the plant cell wall in the complex and, strictly anaerobic rumen ecosystem.